On 23/03/2020 14:38, Steffen Möller wrote:
Dear all,
With the enormous difficulties to get bcbio into our distribution (a
considderable list of sequential dependencies for nim, java libraries,
golang-bio, ....sigh) I also had an eye on nf-core and their
nextflow-based workflows. I think I uploaded the one or other package
from their dependencies but, well, treated it more like an inspiration
than a project. From what I oversee it is far easier to address than bcbio.
[...]
Hi, Steffen.
I've just had a look at the "nf-core" repo and read this:
"please only use Conda as a last resort"
They recommend running "nf-core" under Docker or Singularity, which I
believe would make it unsuitable for packaging as part of "med-bio".
I'm currently running "bcbio_nextgen" under Ubuntu-MATE 18.04 + med-bio,
but the developers advised me NOT to use the 'external' versions of
tools like "bwa" or "bowtie2" from Debian-Med but install everything
isolated from the 'system'.
I think this sort of application is more effort than it's worth to
package for "med-bio". However, I think that a bare-bones package
equivalent to bootstrapping "bioconda" using "miniconda" would be
worthwhile to provide a ready-to-use "bioconda" within Debian-Med.
Bye,
Tony.
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